The purpose of this study was to investigate the antimicrobial activity, antimutagenic and anticancer effects and dyeing properties of the fermented indigo extract. The physiological effects of natural color extracts from colorant plants(gardenia, beet and indigo) were studied. The methanol extract of indigo showed an inhibitory effect on the growth of E. coli and Staph. aureus, and also showed a strong antimicrobial effect on Trich. mentagrophytes compared to others. The methanol extract of indigo showed antimutagenic activities against aflatoxin B1(AFB1) in the Ames test using Salmonella typhimurium TA 100. The proliferation of Clone M-3 mouse melanoma cells and A431 human epidermoid carcinoma cells was inhibited by the methanol extract of indigo. So we decided to use natural indigo for dyeing the fabrics because of those effects. Dried indigo leaves were fermented at variouss temperature and the fermented indigo was reduced by using alkaline(NaOH, Ca(OH)2) and glucose to dye the fabrics. The values of K/S fermented indigo showed the highest value when it was fermented at 3$0^{circ}C$. The indigo fermented at 3$0^{circ}C$ had the greatest number of total bacterial counts and we identified one of the main microorganisms as Aspergillus niger. This microorganism was responsible for the indigo fermentation and accelerated indigo fermentation. So it can be supposed to reduce the fermentation period of indigo by inoculating Aspergillus niger into the indigo leaves at 3$0^{circ}C$.